Slicer Registration Library Case #7: Prostate MRI Cancer Monitoring

Input

exam 1: baseline MRI

exam 1: follow-up MRI

Description

This is an example of serial/logitudinal imaging for change assessment in prostate cancer. We seek to register the follow-up scan to the baseline. Because of the strong changes in image field of view and contrast between the two exams, some additional work is necessary to obtain a good registration: 1) we will first apply a bias field correction to both images, to reduce regional intensity inhomogeneities caused during acquisition by the surface coils. 2) we will generate masks that include only the prostate and a bit of the surroundings. The field of view between the two images is different. When there is content that extends beyond the FOV and the amount differs in both images, leaving that clipped structure unmasked is problematic, particularly for highe DOF registrations, since the registration will try to match the "missing content" by expanding/stretching in that direction. Hence we mask out significant content present only in one image.

Modules used

Download (from NAMIC MIDAS)

Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself.

this should generate a first alignment. note that we need not generate an output volume, because this is an intermediate result, and the BRAINS registration tool will automatically place the moving volume inside the result transform.

Place "Day01_axial_N4" in the background and "Day42_axial_N4" in the foreground. Use fade slider to evaluate the result. In the Data module, verify that the "Day42_axial_N4" image is sitting inside the transform "Xf1_Affine"